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The Genomic Foundation Model (GFM) paradigm is expected to facilitate the extraction of generalizable representations from massive genomic data, thereby enabling their application across a spectrum of downstream applications. Despite…
The AGP format is a tab-separated table format describing how components of a genome assembly fit together. A standard submission format for genome assemblies is a fasta file giving the sequence of contigs along with an AGP file showing how…
Over the last several decades, there has been rapid growth in the number and scope of agricultural genetics, genomics and breeding (GGB) databases and resources. The AgBioData Consortium (https://www.agbiodata.org/) currently represents 44…
Several formats, including FASTA, PIR, GenBank, EMBL, and GCG, have been developed for representing protein sequences composed of natural amino acids. Among these, FASTA remains the most widely used due to its simplicity and human…
The notion of functional dependencies (FDs) can be used by data scientists and domain experts to confront background knowledge against data. To overcome the classical, too restrictive, satisfaction of FDs, it is possible to replace equality…
Biomedical signals are stored in many different data formats. Most formats have been developed for a specific purpose of a specialized community for ECG research, EEG analysis, sleep research, etc. So far none of the existing formats can be…
Inspired by the success of foundation models in applications such as ChatGPT, as graph data has been ubiquitous, one can envision the far-reaching impacts that can be brought by Graph Foundation Models (GFMs) with broader applications in…
Gen3 is an open-source data platform for building data commons. A data commons is a cloud-based data platform for managing, analyzing, and sharing data with a research community. Gen3 has been used to build over a dozen data commons that in…
The Open Annotation Core Data Model specifies an interoperable framework for creating associations between related resources, called annotations, using a methodology that conforms to the Architecture of the World Wide Web. Open Annotations…
With the advance of high-throughput sequencing technologies, it has become feasible to investigate the influence of the entire spectrum of sequencing variations on complex human diseases. Although association studies utilizing the new…
Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical…
Grammar-Guided Genetic Programming (GGGP) employs a variety of insights from evolutionary theory to autonomously design solutions for a given task. Recent insights from evolutionary biology can lead to further improvements in GGGP…
The Gene Ontology (GO) provides biologists with a controlled terminology that describes how genes are associated with functions and how functional terms are related to each other. These term-term relationships encode how scientists conceive…
High quality gene models are necessary to expand the molecular and genetic tools available for a target organism, but these are available for only a handful of model organisms that have undergone extensive curation and experimental…
Graph-structured data pervades domains such as social networks, biological systems, knowledge graphs, and recommender systems. While foundation models have transformed natural language processing, vision, and multimodal learning through…
Biodiversity, the variation within and between species and ecosystems, is essential for human well-being and the equilibrium of the planet. It is critical for the sustainable development of human society and is an important global…
GitHub Copilot, an extension for the Visual Studio Code development environment powered by the large-scale language model Codex, makes automatic program synthesis available for software developers. This model has been extensively studied in…
Many real-world optimization problems are not naturally homogeneous vectors but composite design objects with heterogeneous parameters: integers, real values, Booleans, categoricals, complex-valued descriptors, and embedding vectors.…
The linking genotype to phenotype is the fundamental aim of modern genetics. We focus on study of links between gene expression data and phenotype data through integrative analysis. We propose three approaches. 1) The inherent complexity of…
The Gene Ontology (GO) is a formidable resource but there are several considerations about it that are essential to understand the data and interpret it correctly. The GO is sufficiently simple that it can be used without deep understanding…